[English] 日本語
Yorodumi
- PDB-7yfv: Structure of Rpgrip1l CC1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yfv
TitleStructure of Rpgrip1l CC1
ComponentsProtein fantom
KeywordsPROTEIN BINDING / STRUCTURAL PROTEIN
Function / homology
Function and homology information


thromboxane A2 receptor binding / nose development / retinal rod cell development / neural tube patterning / establishment of planar polarity / lateral ventricle development / head development / ciliary transition zone / pericardium development / photoreceptor connecting cilium ...thromboxane A2 receptor binding / nose development / retinal rod cell development / neural tube patterning / establishment of planar polarity / lateral ventricle development / head development / ciliary transition zone / pericardium development / photoreceptor connecting cilium / axonemal microtubule / negative regulation of G protein-coupled receptor signaling pathway / limb morphogenesis / Hedgehog 'off' state / telencephalon development / Anchoring of the basal body to the plasma membrane / corpus callosum development / olfactory bulb development / non-motile cilium assembly / regulation of smoothened signaling pathway / camera-type eye development / embryonic forelimb morphogenesis / embryonic hindlimb morphogenesis / determination of left/right symmetry / ciliary rootlet / establishment or maintenance of cell polarity / cochlea development / axoneme / cilium assembly / bicellular tight junction / cerebellum development / ciliary basal body / liver development / kidney development / brain development / cilium / cell-cell junction / in utero embryonic development / centrosome / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
RPGR-interacting protein 1, first C2 domain / RPGRIP1 family / RPGRIP1, C-terminal / First C2 domain of RPGR-interacting protein 1 / Retinitis pigmentosa G-protein regulator interacting C-terminal / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.2 Å
AuthorsHe, R. / Chen, G. / Li, Z. / Li, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Iscience / Year: 2023
Title: Structure of the N-terminal coiled-coil domains of the ciliary protein Rpgrip1l.
Authors: He, R. / Chen, G. / Li, Z. / Li, J.
History
DepositionJul 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein fantom
B: Protein fantom
C: Protein fantom
D: Protein fantom


Theoretical massNumber of molelcules
Total (without water)28,5294
Polymers28,5294
Non-polymers00
Water73941
1
A: Protein fantom
B: Protein fantom


Theoretical massNumber of molelcules
Total (without water)14,2652
Polymers14,2652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-10 kcal/mol
Surface area8100 Å2
MethodPISA
2
C: Protein fantom
D: Protein fantom


Theoretical massNumber of molelcules
Total (without water)14,2652
Polymers14,2652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-10 kcal/mol
Surface area8120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.167, 104.674, 38.413
Angle α, β, γ (deg.)90.000, 105.080, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Protein fantom / Nephrocystin-8 / RPGR-interacting protein 1-like protein / RPGRIP1-like protein


Mass: 7132.267 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rpgrip1l, Ftm, Nphp8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CG73
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 7.5% w/v PEG6000, 0.1 M Sodium citrate tribasic dihydrate, pH 4.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 13799 / % possible obs: 99.6 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.03 / Rrim(I) all: 0.08 / Χ2: 0.476 / Net I/σ(I): 4.2 / Num. measured all: 94590
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.246.70.8076900.7860.3320.8740.42899.3
2.24-2.287.10.6276760.8680.250.6760.4599.6
2.28-2.3270.5416750.9060.2170.5830.43999.6
2.32-2.3770.57210.9080.2010.5390.44699.6
2.37-2.4270.4036520.9370.1620.4350.45199.1
2.42-2.4870.366890.9430.1460.3890.46799.4
2.48-2.5470.3257120.960.1310.350.46999.4
2.54-2.616.90.2636540.9730.1070.2840.47299.2
2.61-2.696.70.226890.9730.0910.2380.51499.4
2.69-2.776.30.1837090.9820.0780.1990.49999.7
2.77-2.876.70.1566700.9880.0650.1690.50499.9
2.87-2.997.20.1357080.9920.0540.1460.5299.9
2.99-3.127.20.1086650.9940.0430.1160.50499.7
3.12-3.297.10.0876990.9950.0350.0930.53599.7
3.29-3.4970.0737080.9970.0290.0790.54599.9
3.49-3.766.90.0636710.9970.0260.0680.56399.6
3.76-4.146.30.0516980.9980.0220.0550.525100
4.14-4.746.90.0426960.9990.0170.0460.463100
4.74-5.9770.0447100.9980.0180.0470.394100
5.97-506.40.037070.9990.0120.0330.32999

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.18.2refinement
PDB_EXTRACT3.27data extraction
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.2→29.1 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 28.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2631 690 5.01 %
Rwork0.2138 13086 -
obs0.2163 13776 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.07 Å2 / Biso mean: 57.653 Å2 / Biso min: 30.57 Å2
Refinement stepCycle: final / Resolution: 2.2→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1575 0 0 41 1616
Biso mean---53.74 -
Num. residues----190
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.350.29581440.2522253896
2.35-2.590.2841210.2363261499
2.59-2.960.24811290.2332665100
2.96-3.730.2811410.22062621100
3.73-29.10.24761550.19362648100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2046-4.56023.35445.7261-6.00485.0332-0.0792-0.21960.29790.03480.1661-0.2703-0.1376-0.158-0.1250.4219-0.051-0.04310.48960.03030.5023-4.99236.22915.43
28.6181-4.10376.76713.0597-3.82865.6554-1.08890.70560.9886-0.83960.7530.6528-0.6469-1.21850.29110.5704-0.092-0.07070.58310.10640.6924-5.18915.04227.69
3-0.1615-2.09211.29218.2803-7.05835.57320.02120.10280.1735-0.54490.0631-0.40120.2288-0.29140.10040.3390.01490.04130.360.070.48111.32135.6767.968
42.0867-0.4237-0.28534.11182.26131.33660.2679-2.2518-1.60761.4271-0.21380.08370.0637-0.05150.3080.8858-0.0293-0.15961.2718-0.06470.597321.23230.45430.813
51.99553.71473.80584.82825.08064.1864-0.45950.07820.214-0.55190.27370.2248-0.40660.50790.1350.3902-0.070.00360.437-0.06340.431912.59716.8825.728
63.8337-0.14191.80048.4163-1.15654.66260.8530.81090.25880.41360.32560.2563-0.5298-0.2028-1.09640.74650.0107-0.09450.5901-0.11021.094516.1740.47119.014
71.39931.32071.28085.43296.42738.4237-0.1066-0.18610.21550.66620.10370.26330.9650.35740.12830.39560.005-0.0210.47830.00830.324611.00112.40714.425
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:46 )A3 - 46
2X-RAY DIFFRACTION2( CHAIN B AND RESID 0:5 )B0 - 5
3X-RAY DIFFRACTION3( CHAIN B AND RESID 6:48 )B6 - 48
4X-RAY DIFFRACTION4( CHAIN C AND RESID 1:5 )C1 - 5
5X-RAY DIFFRACTION5( CHAIN C AND RESID 6:47 )C6 - 47
6X-RAY DIFFRACTION6( CHAIN D AND RESID 1:5 )D1 - 5
7X-RAY DIFFRACTION7( CHAIN D AND RESID 6:46 )D6 - 46

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more